blah blah

This file belongs to the repository: https://github.com/drisso/awst_analysis.

The code is released with license GPL v3.0.

(Note: I don’t think we can release these images with GPL license, to be removed from final file) # Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments (Nature) ### Supplementary Figure 3 Visualization of representative benchmarking datasets using t-SNE and UMAP and violin plot of the number of doublets. (a) t-SNE and UMAP visualizations of 4 datasets. From left to right: 10X single cell using 3 cell lines; 10X single cell using 5 cell lines; a CEL-seq2 cell mixture and a CEL-seq2 RNA mixture. Each point represents a cell or ‘pseudo cell’ and the number of cells in each plot is indicated in the title. (b) Violin plot of doublets in each dataset, identified using Demuxlet (DBL: doublet, SNG: single cell). The number of single cells and doublets are shown on top of each violin. Doublets were excluded when calculating the performance metrics.

Supplementary Figure 5: Example clustering results and summary of clustering performance using ARI and the number of clusters.

  1. Examples of clustering results visualized by PCA (top) and t-SNE (bottom), with different colours representing the cluster assignments made by the selected method. The sample sizes are 340 for RNAmix_CEL-seq2, 285 for cellmix3 and 274 for sc_CEL-seq2. Coefficients obtained from linear models fitted using the ARI (b) or the number of clusters (c) as dependent variables, and experimental design, normalization methods, imputation methods and clustering methods as covariates. The coefficients measure whether particular features have positive or negative associations with the dependent variables.

Install and load awst

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("drisso/awst")
#BiocManager::install("GIS-SP-Group/RCA")
#BiocManager::install("hgu133plus2.db")

Setup

library(awst)
library(EDASeq)
library(SingleCellExperiment)

jobName <- "mixoloy20200904"
source(url("https://raw.githubusercontent.com/drisso/awst_analysis/master/functions.R"))

true_number_of_clusters <- c(3, 5, 7, 10, 10)
names(true_number_of_clusters) <- c("sc_10x", "sc_10x_5cl", "RNAmix_celseq2", "cellmix4", "cellmix3")
####
results <- matrix(NA, ncol = 5, nrow = 21)
colnames(results) <- c("where", "what", "silhouette", "NDE", "R2")
k <- 1
save_plots <- FALSE

compute_r2 <- function(y, labs) {
  if(all(y==0)) {
    return(NA)
  }
  fit <- lm(y ~ labs)
  res <- summary(fit)
  return(res$r.squared)
}

get_r2 <- function(datamat, labs) {
  r2 <- apply(datamat, 2, compute_r2, labs)
  return(r2)
}

compute_de <- function(y, labs) {
  if(all(y==0)) {
    return(1)
  }
  fit <- lm(y ~ labs)
  res <- anova(fit)
  return(res[1,5])
}

get_de <- function(datamat, labs) {
  pvals <- apply(datamat, 2, compute_de, labs)
  pvals <- sort(pvals)
  return(datamat[,names(pvals)[1:500]])
}

sc_10x_5cl

prefix <- "sc_10x_5cl"
con <- gzcon(url("https://github.com/LuyiTian/sc_mixology/blob/master/data/csv/sc_10x_5cl.metadata.csv.gz?raw=true"))
annotation.df <- read.csv(textConnection(readLines(con)))
annotation.df$cell.col <- factor(annotation.df$cell_line)
levels(annotation.df$cell.col) <- c("gold", "red", "blue", "magenta", "green3")
annotation.df$cell.col <- as.character(annotation.df$cell.col)
annotation.df$cell_line <- paste0("mix", annotation.df$mix)

con <- gzcon(url("https://github.com/LuyiTian/sc_mixology/blob/master/data/csv/sc_10x_5cl.count.csv.gz?raw=true"))
ddata <- read.csv(textConnection(readLines(con)))

both <- intersect(colnames(ddata), rownames(annotation.df))
ddata <- ddata[, both]
annotation.df <- annotation.df[both,]
prefix <- "sc_10x_5cl"
save(ddata, annotation.df, prefix, file = paste0(prefix, "_counts.RData"))
library(awst)
library(EDASeq)
library(SingleCellExperiment)
load(paste0(prefix, "_counts.RData"))

no_of_detected_gene_per_sample <- colSums(ddata > 0) 
fivenum(no_of_detected_gene_per_sample)
ddata <- EDASeq::betweenLaneNormalization(as.matrix(ddata), which = "full", round = FALSE)
# apply the AWS-transformation 
tmp <- rowSums(ddata)
sum(tmp > 0)
tmp <- colSums(ddata)
sum(tmp > 0)

exprData <- awst(ddata, poscount = TRUE, full_quantile = TRUE)
sum(is.na(rowSums(exprData)))
sum(is.na(colSums(exprData)))

save(exprData, prefix, file = paste0(prefix, "_expression.RData"))

nrow_exprData <- nrow(exprData)
ncol_exprData <- ncol(exprData)

# library(irlba)
# pprcomp <- prcomp_irlba(exprData, 5) # Run PC analysis
# 
# set.seed(2020) 
# ans_Rtsne <- Rtsne(exprData, pca = FALSE) # Run TSNE
# 
# set.seed(2020) 
# ans_umap <- umap(exprData) # Run Umap
# 
# save(nrow_exprData, ncol_exprData, annotation.df,
#      pprcomp, ans_Rtsne, ans_umap, prefix, 
#      file = paste0(prefix, "_expression_working.RData"))

save(nrow_exprData, ncol_exprData, annotation.df, prefix,
     file = paste0(prefix, "_expression_working.RData"))
load(paste0(prefix, "_counts.RData"))
load(paste0(prefix, "_expression.RData"))

# get random subset (to be removed)
set.seed(135)
cellidx <- sample(colnames(ddata), 100)
ddata <- ddata[,cellidx]
annotation.df <- annotation.df[cellidx,]

# awst (exprData)
system.time({
  fq <- EDASeq::betweenLaneNormalization(as.matrix(ddata), which = "full", round = FALSE)
  exprData <- awst(fq, poscount = TRUE, full_quantile = TRUE)
})

user system elapsed 0.223 0.020 0.242

exprData_gf <- awst::gene_filter(exprData, heterogeneity_threshold = .1)
dim(exprData_gf)

[1] 100 6068

# VST
library(DESeq2)

get_hvg <- function(mat, k=1000) {
  vars <- matrixStats::rowVars(mat)
  names(vars) <- rownames(mat)
  vars <- sort(vars, decreasing = TRUE)
  mat <- mat[names(vars)[seq_len(k)],]
  return(mat)
}

dds <- DESeqDataSetFromMatrix(ddata, colData = annotation.df,
                              design = ~1)
# dds <- estimateSizeFactors(dds)
# dds <- estimateDispersions(dds)

system.time({
  vst <- varianceStabilizingTransformation(dds, blind=FALSE)
  vst <- assay(vst)
  vst1000 <- get_hvg(vst, k=1000)
  vst2500 <- get_hvg(vst, k=2500)
  vst5000 <- get_hvg(vst, k=5000)
})

user system elapsed 10.348 6.587 7.013

system.time({
  # rlog
  rld <- rlog(dds, blind=FALSE)
  rld <- assay(rld)
  rld1000 <- get_hvg(rld, k=1000)
  rld2500 <- get_hvg(rld, k=2500)
  rld5000 <- get_hvg(rld, k=5000)
})
## rlog() may take a long time with 50 or more samples,
## vst() is a much faster transformation
user   system  elapsed 

2694.783 4084.403 292.784

# Townes
library(scry)
library(SingleCellExperiment)

system.time({
  sce <- SingleCellExperiment(assays = list(counts = ddata),
                              colData = annotation.df)
  sce <- nullResiduals(sce, assay="counts", type="deviance")
  sce <- nullResiduals(sce, assay="counts", type="pearson")
  
  res_deviance <- assay(sce, "binomial_deviance_residuals")
  # res_deviance <- get_hvg(res_deviance)
  res_pearson <- assay(sce, "binomial_pearson_residuals")
  # res_pearson <- get_hvg(res_deviance)
})

user system elapsed 2.339 4.259 0.346

# CPM
system.time({
  cpm <- t(get_CPM(ddata))
  cpm1000 <- get_hvg(cpm, k=1000)
  cpm2500 <- get_hvg(cpm, k=2500)
  cpm5000 <- get_hvg(cpm, k=5000)
})

user system elapsed 0.062 0.000 0.062

# raw
raw <- as.matrix(ddata)

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
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sc_10x

user system elapsed 0.335 0.008 0.343 [1] 100 15028 user system elapsed 13.720 9.499 9.487

## rlog() may take a long time with 50 or more samples,
## vst() is a much faster transformation
user   system  elapsed 

3933.004 5974.970 429.755 user system elapsed 2.831 4.870 0.404 user system elapsed 0.088 0.000 0.087

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
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## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

RNAmix_celseq2

user system elapsed 0.290 0.002 0.292 [1] 100 6228

## -- note: fitType='parametric', but the dispersion trend was not well captured by the
##    function: y = a/x + b, and a local regression fit was automatically substituted.
##    specify fitType='local' or 'mean' to avoid this message next time.

user system elapsed 21.951 24.092 10.322

## rlog() may take a long time with 50 or more samples,
## vst() is a much faster transformation
## -- note: fitType='parametric', but the dispersion trend was not well captured by the
##    function: y = a/x + b, and a local regression fit was automatically substituted.
##    specify fitType='local' or 'mean' to avoid this message next time.
user   system  elapsed 

2789.856 4126.596 301.494 user system elapsed 2.683 4.702 0.368 user system elapsed 0.079 0.003 0.082

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable

Session info

sessionInfo()
## R version 4.0.0 (2020-04-24)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] cluster_2.1.0               scry_1.0.1                 
##  [3] DESeq2_1.28.1               SingleCellExperiment_1.10.1
##  [5] EDASeq_2.22.0               ShortRead_1.46.0           
##  [7] GenomicAlignments_1.24.0    SummarizedExperiment_1.18.2
##  [9] DelayedArray_0.14.1         matrixStats_0.56.0         
## [11] Rsamtools_2.4.0             GenomicRanges_1.40.0       
## [13] GenomeInfoDb_1.24.2         Biostrings_2.56.0          
## [15] XVector_0.28.0              IRanges_2.22.2             
## [17] S4Vectors_0.26.1            BiocParallel_1.22.0        
## [19] Biobase_2.48.0              BiocGenerics_0.34.0        
## [21] awst_0.0.4                  knitr_1.28                 
## [23] BiocManager_1.30.10        
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-6           bit64_0.9-7            RColorBrewer_1.1-2    
##  [4] progress_1.2.2         httr_1.4.1             tools_4.0.0           
##  [7] R6_2.4.1               colorspace_1.4-1       DBI_1.1.0             
## [10] tidyselect_1.1.0       prettyunits_1.1.1      bit_1.1-15.2          
## [13] curl_4.3               compiler_4.0.0         rtracklayer_1.48.0    
## [16] scales_1.1.1           genefilter_1.70.0      askpass_1.1           
## [19] rappdirs_0.3.1         DESeq_1.39.0           stringr_1.4.0         
## [22] digest_0.6.25          rmarkdown_2.2          R.utils_2.9.2         
## [25] jpeg_0.1-8.1           pkgconfig_2.0.3        htmltools_0.4.0       
## [28] umap_0.2.5.0           dbplyr_1.4.4           rlang_0.4.6           
## [31] RSQLite_2.2.0          generics_0.0.2         jsonlite_1.6.1        
## [34] hwriter_1.3.2          dplyr_1.0.0            R.oo_1.23.0           
## [37] RCurl_1.98-1.2         magrittr_1.5           GenomeInfoDbData_1.2.3
## [40] Matrix_1.2-18          munsell_0.5.0          Rcpp_1.0.4.6          
## [43] reticulate_1.16        lifecycle_0.2.0        R.methodsS3_1.8.0     
## [46] stringi_1.4.6          yaml_2.2.1             MASS_7.3-51.6         
## [49] zlibbioc_1.34.0        BiocFileCache_1.12.1   grid_4.0.0            
## [52] blob_1.2.1             crayon_1.3.4           lattice_0.20-41       
## [55] splines_4.0.0          GenomicFeatures_1.40.1 annotate_1.66.0       
## [58] hms_0.5.3              locfit_1.5-9.4         pillar_1.4.4          
## [61] geneplotter_1.66.0     biomaRt_2.44.1         XML_3.99-0.3          
## [64] glue_1.4.1             evaluate_0.14          latticeExtra_0.6-29   
## [67] png_0.1-7              vctrs_0.3.1            gtable_0.3.0          
## [70] openssl_1.4.1          purrr_0.3.4            assertthat_0.2.1      
## [73] ggplot2_3.3.1          xfun_0.14              aroma.light_3.18.0    
## [76] xtable_1.8-4           RSpectra_0.16-0        survival_3.1-12       
## [79] glmpca_0.2.0           tibble_3.0.1           AnnotationDbi_1.50.3  
## [82] memoise_1.1.0          ellipsis_0.3.1

Table

where what silhouette NDE R2
raw sc_10x_5cl 0.0666 500 0.5448
cpm sc_10x_5cl 0.0462 500 0.5693
awst sc_10x_5cl 0.0990 500 0.5141
vst sc_10x_5cl 0.0731 500 0.5983
rlog sc_10x_5cl 0.1427 500 0.6014
deviance sc_10x_5cl 0.1370 500 0.5906
pearson sc_10x_5cl 0.1232 500 0.5546
raw sc_10x 0.1194 500 0.6635
cpm sc_10x 0.0734 500 0.6840
awst sc_10x 0.1286 500 0.6588
vst sc_10x 0.1207 500 0.6984
rlog sc_10x 0.1567 500 0.7015
deviance sc_10x 0.2050 500 0.6724
pearson sc_10x 0.1677 500 0.6251
raw RNAmix_celseq2 -0.0415 500 0.3194
cpm RNAmix_celseq2 -0.0151 500 0.3718
awst RNAmix_celseq2 -0.0083 500 0.3458
vst RNAmix_celseq2 -0.0184 500 0.4259
rlog RNAmix_celseq2 0.0118 500 0.4378
deviance RNAmix_celseq2 0.0093 500 0.4376
pearson RNAmix_celseq2 0.0086 500 0.4343
knitr::knit_exit()